Your wife wants Swedish citizenship with female gender. Having "female gender" will be much much more important than having the same gender in two passports.

Most countries want to see one passport. They will check one passport, and only one passport, and check if there is anything suspicious or unusual about the password. There's nothing unusual about your wife having a Swedish + female passport. It would be unusual for your female looking wife to have a Thai + male passport. Or a Swedish + male passport. So she can show her Swedish passport and should have no problems.

(In the situation described in the linked article, your wife would have been fine with her Swedish + female passport, but not with Thai + male, and quite possibly not with two passports).

Your wife wants Swedish citizenship with female gender. Having "female gender" will be much much more important than having the same gender in two passports.

Most countries want to see one passport. They will check one passport, and only one passport, and check if there is anything suspicious or unusual about the passport. There's nothing unusual about your wife having a Swedish + female passport. It would be unusual for your female looking wife to have a Thai + male passport. Or a Swedish + male passport. So she can show her Swedish passport and should have no problems.

(In the situation described in the linked article, your wife would have been fine with her Swedish + female passport, but not with Thai + male, and quite possibly not with two passports).